Table 1 Reference genomes used in this study
From: Combining multiple functional annotation tools increases coverage of metabolic annotation
Genome Name | Biocyc ID | Phylum | NCBI Accessions | Proteins |
|---|---|---|---|---|
Mycobacterium tuberculosis CDC1551 | MTBCDC1551 | Actinobacteria | AE000516 | 4189 |
Mycobacterium tuberculosis H37Rv | MTBH37RV | Actinobacteria | AL123456 | 4018 |
Streptomyces coelicolor A3(2) | SCO | Actinobacteria | NC_003888, NC_003903, NC_003904 | 8152 |
Bacteroides thetaiotaomicron VPI-5482 | BTHE | Bacteroidetes | AE015928, AY171301 | 4825 |
Candidatus Cardinium hertigiib | CBTQ1 | Bacteroidetes | HG422566, CBQZ010000001- CBQZ010000011 | 739 |
Synechococcus elongatus PCC 7942 | SYNEL | Cyanobacteria | CP000100, CP000101 | 2661 |
Listeria monocytogenes 10403S | 10403S_RAST | Firmicutes | CP002002 | 2814 |
Bacillus anthracis Ames | ANTHRA | Firmicutes | NC_003997, AE017335, AE017336 | 5602 |
Bacillus subtilis 168 | BSUB | Firmicutes | AL009126 | 4185 |
Clostridium saccharoperbutylacetonicum ATCC 27021 | CLOSSAC | Firmicutes | CP004121, CP004122 | 5821 |
Eubacterium rectale ATCC 33656 | EREC | Firmicutes | CP001107 | 3626 |
Clostridioides difficile 630 | PDIF272563 | Firmicutes | AM180355, AM180356 | 3809 |
Agrobacterium fabrum C58 | AGRO | Proteobacteria | AE008687, AE008688, AE008689, AE008690 | 5402 |
Aurantimonas manganoxydans SI85-9A1 | AURANTIMONAS | Proteobacteria | AAPJ01000001- AAPJ01000035 | 3650 |
Caulobacter crescentus CB15 | CAULO | Proteobacteria | AE005673 | 3737 |
Caulobacter crescentus NA1000 | CAULONA1000 | Proteobacteria | CP001340 | 3885 |
Escherichia coli CFT073 | ECOL199310 | Proteobacteria | AE014075 | 5379 |
Escherichia coli K-12 substr. W3110 | ECOL316407 | Proteobacteria | NC_007779 | 4410 |
Escherichia coli B str. REL606 | ECOL413997 | Proteobacteria | CP000819 | 4209 |
Escherichia coli K-12 substr. MG1655a | ECOLI | Proteobacteria | U00096 | 4140 |
Escherichia coli O157:H7 str. EDL933 | ECO0157 | Proteobacteria | AE005174, AF074613 | 5449 |
Candidatus Evansia muellerib | EVA | Proteobacteria | LM655252 | 330 |
Helicobacter pylori 26,695 | HPY | Proteobacteria | CP003904 | 1594 |
Methylosinus trichosporium OB3b | MOB3B | Proteobacteria | NZ_ADVE02000001- NZ_ADVE02000003 | 4344 |
Candidatus Portiera aleyrodidarum BT-QVLCb | PABTQVLC | Proteobacteria | CP003867 | 280 |
Shigella flexneri 2a str. 2457 T | SHIGELLA | Proteobacteria | AE014073 | 4068 |
Vibrio cholerae O1 biovar El Tor str. N16961 | VCHO | Proteobacteria | AE003852, AE003853 | 3828 |